Comparative Bioinformatics and TP53 Expression

比较生物信息学和 TP53 表达

• 批准号: 6969522
• 负责人: PETER J WADDELL
• 金额: $ 29.54万
• 依托单位: UNIVERSITY OF SOUTH CAROLINA AT COLUMBIA
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-09-30 至 2010-09-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6969522
• 关键词: DNA footprinting; animal genetic material tag; biochemical evolution; bioinformatics; cell line; computational biology; fibroblasts; functional /structural genomics; gene expression; genetic regulatory element; human genetic material tag; nucleic acid sequence; p53 gene /protein; regulatory gene; reporter genes; site directed mutagenesis; species difference

DESCRIPTION: Innovative interdisciplinary work is essential to address the most challenging issues in the era of genomic biomedical research. One of these is the evolutionary structure/function of transcriptional regulation. Comparative molecular evolutionary work is essential here. TP53 is probably the single most important gene in cell cycle and cancer studies. However, there is no clear model for the evolution of the main transcriptional regulatory region across mammals, nor how our key animal models, including mouse, differ. Going from a shrew-like ancestor to an elephant, a whale or a human implies important changes in the regulation of TP53. While many mammals retain a similar TP53 cis-regulatory region to humans, evidence of its overall importance, others have undergone large changes, e.g., mice are highly atypical and one close relative of primates has deleted nearly the whole 5' regulatory region. This project's aims are as follows: (1) Very dense comparative alignment of the TP53/GBN5 cis-regulatory region across mammals; (2) Characterization of transcriptional responses using cell lines from a wide variety of species; (3) Molecular footprinting of this promoter region across mammals; (4) Test hypotheses of regulatory evolution using deletion/site-directed mutation constructs with reporter gene assays. As with (2) a key novel aspect of this work is the use of wildtype fibroblast cell lines from many different orders of mammals; (5) Using a novel pair-wise cell line assay, separate cis (local) from trans (non-local) effects in the evolution of transcriptional regulation; (6) Use, test, and develop bioinformatic/genomic and molecular evolutionary techniques on the dense sequence alignment of (1), plus genomes of over 14 species of mammals. To compare and contrast their effectiveness with our direct molecular data, Overall, to arrive at a better understanding of this important regulatory region and to illustrate the enhanced potential of comparative bioinformatics/genomics plus comparative functional molecular biology.

描述： 创新的跨学科工作对于解决基因组生物医学研究时代最具挑战性的问题至关重要。其中之一是转录调控的进化结构/功能。比较分子进化工作在这里至关重要。 TP53 可能是细胞周期和癌症研究中最重要的一个基因。然而，哺乳动物主要转录调控区域的进化尚无明确的模型，也没有我们的关键动物模型（包括小鼠）有何不同。从类似鼩鼱的祖先到大象、鲸鱼或人类，意味着 TP53 的调控发生了重要变化。虽然许多哺乳动物保留了与人类相似的 TP53 顺式调节区，这证明了其整体重要性，但其他哺乳动物却经历了巨大的变化，例如小鼠是高度非典型的，灵长类动物的一种近亲删除了几乎整个 5' 调节区。该项目的目标如下：（1）跨哺乳动物TP53/GBN5顺式调控区的非常密集的比较比对； (2) 使用来自多种物种的细胞系表征转录反应； (3) 哺乳动物中该启动子区域的分子足迹； (4) 使用缺失/定点突变构建体和报告基因测定来测试调控进化的假设。与（2）一样，这项工作的一个关键的新颖方面是使用来自许多不同目的哺乳动物的野生型成纤维细胞系； (5) 使用新型成对细胞系测定，将转录调控进化中的顺式（局部）效应与反式（非局部）效应分开； (6) 在 (1) 以及超过 14 种哺乳动物的基因组的密集序列比对上使用、测试和开发生物信息学/基因组和分子进化技术。总体而言，将它们的有效性与我们的直接分子数据进行比较和对比，以更好地理解这一重要的调控区域，并说明比较生物信息学/基因组学和比较功能分子生物学的增强潜力。